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Comparing Fidelity and Performance of Proofreading PCR Enzymes

itor recently introduced a new proofreading PCR enzyme, called PLATINUM Pfx DNA polymerase. Contrary to its trade name, Pfx was derived from the Pyrococcus sp. strain KOD1 (P. sp. KOD) rather than Pyrococcus furiosus (Pfu), the source of Pfu DNA polymerase. KOD DNA polymerase was first described by Tagaki, et al.6, and commercialized for PCR by Toyobo. Phylogenetic analyses have shown that, although reportedly from a Pyrococcus isolate,6 KOD DNA polymerase is more closely related to enzymes from Thermococcus species (e.g., Vent, 9N-7) than Pyrococcus species (Pfu, Deep Vent).7 According to its manufacturer, the Pfx version of KOD DNA polymerase possesses hot start capability provided by neutralizing polymerase antibodies.

The manufacturers claimed that Pfx DNA polymerase exhibits greater accuracy than Pfu DNA polymerase8 (authors cite Tagaki, et al.6). Pfx was also reported to provide comparable sensitivity and higher amplification specificity compared to PfuTurbo DNA polymerase.8 In this report, we present the results of direct fidelity and PCR performance comparisons between PfuTurbo DNA polymerase and Pfx DNA polymerase. PCR performance is assessed with respect to product yield, sensitivity, specificity, and target-length capability.

PCR Fidelity Comparisons

PCR enzyme fidelity has been measured using a number of different methods, including DGGE analyses3 and monitoring phenotypic changes in mutational target genes (lacI1 and p53 2). These studies showed that Pfu DNA polymerase exhibits the lowest intrinsic error rate of any commercial thermostable DNA polymerase. For example, using a PCR mutation assay based upon the lacIOlacZa target gene,1 Pfu DNA polymerase exhibited an average error rate 2-fold lower than that of Vent and Deep Vent DNA polymerases,1 3- to 6-f
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